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- PDB-6xpq: Human antibody D1 H1-17/H3-14 in complex with the influenza hemag... -

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Basic information

Entry
Database: PDB / ID: 6xpq
TitleHuman antibody D1 H1-17/H3-14 in complex with the influenza hemagglutinin head domain of A/Texas/50/2012(H3N2)
Components
  • Hemagglutinin
  • antibody D1 H1-17/H3-14 heavy chain
  • antibody D1 H1-17/H3-14 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody antigen complex / influenza / hemagglutinin / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsMcCarthy, K.R. / Harrison, S.C.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117892 United States
CitationJournal: Mbio / Year: 2021
Title: A Prevalent Focused Human Antibody Response to the Influenza Virus Hemagglutinin Head Interface.
Authors: McCarthy, K.R. / Lee, J. / Watanabe, A. / Kuraoka, M. / Robinson-McCarthy, L.R. / Georgiou, G. / Kelsoe, G. / Harrison, S.C.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
C: antibody D1 H1-17/H3-14 light chain
B: antibody D1 H1-17/H3-14 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1776
Polymers82,4173
Non-polymers1,7603
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-3 kcal/mol
Surface area34820 Å2
Unit cell
Length a, b, c (Å)115.360, 162.800, 202.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hemagglutinin


Mass: 32618.846 Da / Num. of mol.: 1 / Fragment: head domain (UNP residues 53-335)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Texas/50/2012(H3N2))
Strain: A/Texas/50/2012(H3N2) / Gene: HA, L998_47834gpHA / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4L1D1
#2: Antibody antibody D1 H1-17/H3-14 light chain


Mass: 23168.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody antibody D1 H1-17/H3-14 heavy chain


Mass: 26629.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.76 Å3/Da / Density % sol: 78.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.5 M lithium chloride, 1.0 M sodium citrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2019
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4.2→49.105 Å / Num. obs: 13796 / % possible obs: 96.58 % / Redundancy: 3.7 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1066 / Rpim(I) all: 0.06226 / Rrim(I) all: 0.1241 / Net I/σ(I): 7.62
Reflection shellResolution: 4.2→4.35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.9088 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 1386 / CC1/2: 0.639 / CC star: 0.883 / Rpim(I) all: 0.5109 / Rrim(I) all: 1.047 / % possible all: 98.16

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5W08 & 6E4X

5w08

6e4x


Resolution: 4.2→49.105 Å / SU ML: 0.69 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3065 696 5.05 %
Rwork0.2727 13084 -
obs0.2744 13780 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 384.83 Å2 / Biso mean: 236.6196 Å2 / Biso min: 133.66 Å2
Refinement stepCycle: final / Resolution: 4.2→49.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5426 0 117 0 5543
Biso mean--295.49 --
Num. residues----704
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.2003-4.52440.3971210.3545264098
4.5244-4.97930.34251520.3061258798
4.9793-5.69890.32771200.2954257896
5.6989-7.17640.32951530.3137262897
7.1764-49.1050.27041500.2291265195

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